Chozo Identity Crisis
by Inoctutalie
Summary: With the planet Phaaze destroyed, and all Phazon with it, Samus Aran sets a course for the Galactic Federation. An unkown spaceship lurks behind, waiting for a chance...Samus will be confronted with a struggle for power, one that will change her life. R
1. Confrontation

Disclaimer: I don't own the copyrights to Metroid, but the person who does is probably a very rich man. I will use characters in and from the Metroid series, but I do not take credit for making them up, although I do take credit for the characters I do make up, like General Kreejn and Commander Ihkiyuk. There will be other characters introduced in this Fan-Fic, those existing in the series and those not. I will also take several liberties with this story, so don't bug me about accuracy like a half-blind bookish scholar (stereotype!) who tries to point out that Samus is really a guy, and has no idea what the heck he's talking about. So, with further ado, enjoy this Fan-Fic. (Or not. It kinda depends on what mood you're in….)

_"We have a visitor" _Adam chimed.

Great. Another task, another week of battling and destroying. Heaving a great sigh, Samus Aran, the great bounty hunter of the Galactic Federation, settles back into her command chair, glancing at the other pilot chair to her left. Empty, as usual.

_"The ship is a stolen Federation craft, the Delano 7, piloted by Sylux. Target is closing fast. Evasive maneuvers recommended."_

"Not yet, Adam. Let's see what he wants first. Change course to a the nearest planetoid without harmful atmosphere. Open a channel with our visitor."

_"Yes, Ma'am"_

Suddenly finding the soft command chair uncomfortable, Samus pushed herself up and paced in front of the video screen. Realizing she shouldn't embarrass herself in front of another bounty hunter in her zero suit, she quickly went over to the transparent field behind which her Varia suit was kept. Beside it were other suits, collected over her missions. She preferred the Varia suit most. It felt natural. Punching in a quick command into a side panel, the suit, as if by magic, materialized from behind the storage container to cover Samus's body, conforming itself to her figure and booting up systems. That done, she casually placed herself in a daunting position in front of the view screen.

_"Connection made. Visual in a few seconds"_

"Thank you, Adam. That will be all for a while," Samus spoke clear and direct, the words coming without thinking.

The screen went black, and slowly materialized into a figure, the background shrouded in darkness. The figure was clad in a blue suit with shoulder spikes, with no attached arm weapons, and glowing green lines running up and down the body. The helmet was blue, with a T of green lines to serve as a small visual connection to the surrounding world.

"So, Samus Aran, we meet again. You disappoint me, fighting for a power-hungry government. I thought you would know better than that," Sylux's cool words and soft-spoken voice send chills down Samus's back; the voice was strangely familiar.

"What do you want, Sylux? You have the chance to surrender yourself now, or I'll have to arrest you for stealing, murder,…"

"Ha, ha, ha, ha," Sylux's cold laugh shoves a dagger of ice through Samus's heart. "You don't learn easy, do you? I'm not here to surrender. I'm here to level debts. You owe the space pirates, and I'm here to collect the payment. So prepare yourself for battle, Samus Aran. I'll be waiting."

The screen blacked out, leaving Samus looking at a reflection of herself in the black void that was space. An interesting proposal he had. This wasn't an assignment, and she could use some relax time.

_"Target changing course. Current trajectory is aimed at the planetoid you set as a destination earlier. Change in course recommended"_

Samus frowned. Why would Adam recommend a change in course? He had heard the battle proposal just as clearly as she had. Samus opened her mouth to speak, but instead walked over to a recharge station, where she selected weapons she would want, and punched the nozzle of her arm cannon into a special port, quickly downloading the information and ammo supplies. She then sat down in the command chair and waited to land.

* * *

General Kreejn paced in front of the view screen. He occasionally stopped to check various instruments, fine tuning them again and again. He stopped and glared down a soldier who had just entered the room. General Kreejn was a Space Pirate to be reckoned with. His broad shoulders and head spikes made him a fearsome sight. He was fierce in battle and diplomacy, a force only second to Ridley, his commanding officer. With his commanding officer currently undergoing regeneration processes, he was in charge.

"Well, soldier, speak or I'll rip your tongue out with my toes, after you're long dead! Don't just stand there, talk to me!" Kreejn's vice echoed around the room as he towered over the cowing soldier. All movement froze as the surrounding Space Pirates watched in high amusement.

"Sylux has confirmed contact with enemy Samus Aran, and is landing on nearby planetoid. Visual in a few minutes. Samus Aran is following," the unfortunate soldier replied.

Kreejn glared at him, and the terrified soldier scurried away as the surrounding officers and commanders laughed. Scowling at everyone else, the general soon gained silence from the crowd of military personnel. Gradually returning to the usual business, the room filled with the sound of work. Kreejn liked that sound; it meant progress was being made. He returned to his console. Sylux was being used to get to Samus's DNA. If only he knew how he was being manipulated to get to Samus. Oh, well. This would all be done with shortly, with him in command of the Space Pirates. Grinning wickedly, he imagined what kind of power that would give him. But Ridley would have to be taken care of. No, that would not give him satisfaction. He would need to do better than that. Thinking hard, he exited the command room and made his way back to his private quarters. He needed to think this out. Every detail.

* * *

The landing gear engaged and pushed against the hard stone as the ship lowered itself with expert precision into the rough canyon floor. Samus was raised via an energy lift from the cockpit to the outside world, and she stretched, enjoying the freedom each world visit allowed her. Then, focusing on her self-given mission, she departed for Sylux's ship.

* * *

Sylux relaxed on the large rock he had perched upon. He switched to his energy visor, which received all kinds of different energy and recognized different energy signatures automatically. He set it to receive electrical impulses, and watched Samus's suit, outlined by its energy signature, through the canyon walls as she made her way to the wide area he had selected for their battleground.

* * *

Samus stopped. Something wasn't right. A feeling deep inside her surfaced, a feeling that had saved her countless times from ambushes and attacks. She continued with caution, scoping out each area before going on.

* * *

Sensing the element of surprise was gone, Sylux stood up and moved to the top of a boulder in the center of the canyon, in plain sight, and waited.

* * *

Halting at the beginning of a turn, Samus stopped and switched visors. The Dark Visor worked best in dark areas, but it would also highlight her enemies in bight red, giving her an advantage in accuracy. After she did that, she launched herself around the bend, arm cannon charged and ready to fire.

Sylux watched in half amusement as Samus dove around the corner, charging a shot. He shook his head and jumped off the boulder.

"Samus Aran, I was beginning to think you weren't going to show up," Sylux chided.

"You won't be so cocky when I'm done with you, Sylux. I let you get away back in the Alimbic system. I won't be so lenient this time," Samus replied.

"Really? I thought you were just too slow to catch up. But, on to business. The rules of this battle are simple. Power beam, missiles, and one affinity weapon. Any other weapons are banned, on your honor. But since you don't have a natural affinity weapon, I'll let you choose one. Any suit technology is legit. Oh, and one more thing; I won't be going easy this time," Sylux pointed his arm cannon barrel at Samus as he said the last words, a challenge any hunter would recognize instantly.

Samus quickly scanned Sylux; something was different about him. Suit expansion? Modification? Samus would soon find out. A 2-D image dominated half of Samus's visor. It displayed a stolen Federation technology suit, with dual arm cannons. Dual arm cannons? Last time, he had only one. Grapple beams, new visors, more powerful beam weapons, and a new technology she had not encountered before. She was going to enjoy this fight. Smiling to herself, Samus returned the arm cannon challenge, and quickly fired several shots at Sylux.

Sylux dodged to the side, Samus's shots following him as he ran a circle around her. He shot a grapple towards the top of the canyon about 50 feet up, catching the edge of the cliff. Pulling himself up, he reached the edge and clambered over. Disappearing out of sight, Sylux quickly engaged his left arm cannon and started to charge missiles in both cannons. Meanwhile, Samus attempted the same feat, pulling herself up her own grapple beam. Sylux leaned over the cliff and shot both charged shots directly at Samus, who was almost at the top. Unable to move out of the way, Samus took both hits and engaged morph-ball mode, hitting the ground with a sickening thud.

Jumping off the canyon edge, Sylux curled up and transformed into Lockjaw, his alternate form. His dual blades pointed at the ground, Sylux rushed towards Samus. Rolling away quickly, Samus changed out of morph-ball, stood up and charged her missile. Missing his target, Sylux quickly hovered away, down the center of the canyon. Sensing he was running away, Samus fired the charged missile after him, missing by inches. Sylux sped towards a distant cave in the canyon wall, disappearing into it as Samus took aim. With her dark visor, Samus could see Sylux clearly, but then Sylux activated a disruptor in his suit, causing Samus to see nothing but popcorn static. Switching visors, Samus stopped running and peered into the gloom.

Sylux watched her as she tried to make out images in the darkness. He stood perfectly still, even as she fired into the dark, hoping to get a lucky shot. Seeing that she wasn't going anywhere with that tactic, she switched weapons. Sylux readied his dual blasters, preparing to annihilate Samus.

Samus took careful aim with the Imperialist. The zoom capability helped her take precise shots. She had picked it up in the Alimbic system, and knew from experience that Sylux was vulnerable to the Imperialist's shots.

Sylux grew tired of waiting. He shifted his wait from one foot to another.

Her eyes accustomed to the darkness in the cave ahead of her, Samus stood very still, waiting for movement. As Sylux shifted his weight, Samus pulled the trigger. The red beam shot out of her arm cannon, the noise of the shot echoing off the canyon walls, sending a flock of airborne creatures in the opposite direction.

Sylux took the shot in the neck. It wasn't a head shot, but it was nearly as bad as one. Sylux's vision swam, and he swooned. Dazed, he began charging his arm cannons.

Samus charged him, ramming into him. Knocked off balance, he fell to the ground. Samus charged her arm cannon and pointed it at his head.

Sylux opened his eyes to be greeted by a large ball of energy on the end of Samus's arm cannon. Realizing he had to surrender or die, he shut off his weapons systems. Relaxing, Samus let the charge diminish until the large ball of energy went away. Then, Sylux rapidly kicked Samus in the chest and stood up. Samus, stumbling back, raised her arm cannon in self-defense. Having no mercy, Sylux repeatedly kicked and punched Samus, until she was sprawled on the floor struggling to breathe.

Sylux turned his weapon systems back on. Charging a missile, he looked around the cave. It was eerily quiet on this planet, although scans had detected large amounts of animal life in this region. Hearing movement, he turned back to his nearly dead foe. Samus was standing up, breathing heavily. He smiled behind his visor as he took aim at her head. Her visor was bright blue. All her lights shone blue, and a shadow of a face appeared in the aquamarine visor. The face was not Samus's. Sylux backed away, refusing to believe it. Samus advanced and delivered a crushing blow to his head with the end of her arm cannon.

* * *

"Stop it! Stop the image right there. What is that?" demanded Kreejn.

"That's Samus Aran, sir," replied Commander Ihkiyuk.

"I know that much! But the face, I know that face! Enlarge the visor! Now!"

Ihkiyuk complied. The image zoomed in on Samus's visor. The image there froze all activity faster than if Kraid had walked into the room, or rather, tried. The face in Samus Aran's visor was unmistakable. It was a skull, made of the one substance all had thought gone forever with the recent destruction of the planet Phaaze_. Phazon_. (Spoiler!)


	2. Adam's Moment

The silence in the control room was profound

The silence in the control room was profound. The first to break the silence was Commander Ihkiyuk.

"I thought Dark Samus was gone, destroyed forever, with the Phazon," he said.

General Kreejn was speechless. Dark Samus was not supposed to be alive!

"We've lost visual with Sylux. He is badly damaged, and unconscious," reported an officer standing next to a glowing screen showing transmissions from Sylux's ship.

"Well, we can only wait until Sylux can contact us again," Kreejn managed to speak, "Meanwhile, I'll be in my private quarters. Soldier; arrange a meeting with the Council. Tell them I've a proposal they'd like to hear. Now, move it, before I decide to decapitate you!"

"Yes, sir! Right away, sir!" the soldier replied, hurrying off to do the General's bidding.

* * *

Samus opened her eyes. She was in her ship, lying on the floor. Her head hurt when she tried to stand up, so she just stayed on the floor.

"Adam, how did I get back here?"

"You came here, carrying the bounty hunter Sylux. You placed him behind a high-level security containment shield, and collapsed on the floor. You've been there for several hours"

"Really? I don't remember a thing. Last I remember, I was on the cave floor."

Shaking her head, she tried to stand up again. The headache came back, but she was able to shake it off. Stumbling over to the command chair, she sat down.

"Fighting for the Federation, and not for Freedom? Your father would be disappointed," said a voice somewhere behind her.

Samus spun in her chair. Behind a clear wall reinforced with electrical energy and shields was Sylux. He was sitting on a bunk with clean sheets, watching Samus closely.

"How would you know what my father would or would not think of me?" Samus shot back.

"I knew him once," Sylux responded, not saying any more.

"What do you know? Tell me, Sylux," Samus demanded.

Sylux said nothing, but lay down on the cot and looked to be asleep.

Samus, frustrated as ever, turned in her chair and started typing random commands in the ship's computer.

* * *

Sylux lay very still. He knew it would agitate Samus. Glancing around, seeing that she was busy at the console, Sylux sat up. Studying her from the bed, Sylux thought. He thought about the experience in the cave, and what it might mean. His hatred for her and the Federation still burned bright, but he was curious. He could use Samus to his own advantage. He need only wait until the perfect moment to strike...

Calming down, Samus began to think clearer thoughts. Sylux was in her ship, trapped under her constant supervision. She should call the Federation. Let them know where she was, and who she had in custody. She started to type commands, and realized she could have Adam do it for her.

"Adam, please open a channel with Federation Headquarters. Set the priority level to level red."

Samus waited. No response. Frowning, she called, "Adam? Are you there?"

No response. That was weird. Adam always responded. According to the console that monitored her ship, everything was functioning normally.

Realizing Sylux must have something to do with it, she turned around and stood up from her chair.

Sylux was sitting up, alert as ever.

"What have you done with my computer? Why isn't Adam responding?"

Standing up, Sylux shot back, "I haven't done anything to your ship, much less your incompetent computer."

Fuming, Samus had half a mind to let the shield down and kill him right there. But then, the Federation wouldn't be too happy with a dead prisoner. Shaking her head, she turned back to her main visual screen. Something wasn't right, and she was going to find out what.

Adam, oblivious to Samus's commands, remained in inner turmoil. Computers weren't supposed to struggle with emotional problems. He had never had an emotion, just the programmed responses that this Adam character would have. But, even as he refused to admit it, Samus and he had developed a personal computer-human relationship, one that he could not be programmed with. He did not trust Sylux, he knew that he was going to try something dangerous that would endanger both Adam and Samus.

Finally returning to the world, Adam checked visual cameras. Samus was looking at the main visual screen, apparently confused. To help both him and Samus, Adam inquired, "_Samus, are you alright?"_

'"Adam, I've been calling to you for the past hour. I've tried the lesser systems, but I can't open a channel without you. I need to contact Headquarters, and let them know we have a prisoner."

"_I can do that. Priority level?"_

"Red."

"_Message sent. Awaiting response."_

"Good. Let me know when we have visual."

* * *

"That, gentlemen, is my proposal. It may sound a little risky, but in the long run, it would be well worth it," General Kreejn waited for a response from the council. He had told them the full plan, and not one had spoken yet. He almost wondered if they were dead, just sitting in their chairs, bored to death. Then one stood up and addressed Kreejn.

"I believe I speak for the whole council when I say that though it is risky, I believe it can be done. Since you are in command as of now, it is up to you whether or not to proceed. It would be best if each soldier was given a choice ahead of time, so that they may decide for themselves if they want to change their entire genome," the Councilor said very slowly.

Kreejn could not hide his excitement. Steps had already been taken towards his goal; he needed only the permission of the Council. Putting on a straight face, he responded, "Thank you, wise Council. You have made a decision that will affect all of Space Pirate history."

Bowing, Kreejn left the council room. He would take the operation to the next level as soon as he could.

_"General Kreejn, you are needed at the command center immediately."_

The voice came from the overhead speakers that adorned the Space Pirate halls. He picked up his pace. This had better be good.

* * *

While Adam sent the transmission, Samus stared at Sylux. Still suspicious, she tried to see into him, understand him. Tried to see things from his perspective: What did he want? Why was he so angry?

"Connection made. Visual in a few seconds."

Turning, Samus prepared to talk to the Federation.

* * *

"What is it?" General Kreejn shouted. Startled, the crew turned towards him.

"We've intercepted a transmission from Samus's star ship. She's contacting the Federation," one officer replied.

"Good. Now get to work unscrambling the message. I want visual in half an hour. That should give you plenty of time, you ugly freaks of nature."

Insulted, the crew knew better than to respond to this threat. Turning back to their consoles, they went back to work.

Adam closed the link to Federation Headquarters. Samus turned to Sylux.

"Now tell me, how do you know my father?" Samus spoke clearly and precise. She wanted a straight answer, and if Sylux didn't give her one, she might not have to return to Headquarters. She wanted to question him here, now, and not with their session being monitored by the Federation.

Sylux sighed inwardly. He couldn't reveal too much. He would have to make his move now.

"I can't tell you now, but I can tell you that he would be disappointed. You are fighting for a power-hungry government, one that will be the downfall of civilization as you know it. You can't fight for these people, Samus. They will be destroyed, and you with it. You need to decide which side to be on, Samus Aran. Your life depends on it."

Samus blinked. He didn't answer her question the way she wanted him to. Thinking about what he said, she could see how his twisted perception could allow him to see the Federation as a power-hungry government. Opening her mouth to speak, she stopped herself.

Seizing moment, Sylux jumped in, "You are no different than me, Samus. Fighting for what you think is right. Finding justice everywhere you go. That is not how life works, Samus. You need to be mean every once in a while. You need to take matter into your own hands. You are but a pawn in this, Samus Aran. You need to decide right now, are you going to take that, or are you going to use it to your own advantage? Decide, Samus Aran. Think of your father."

Through all of this, Adam had remained quiet. Now, he put in his own opinoin, if computers could have opinions.

"Samus, he is trying to use you. He is lying to you, spinning a web of deceit," Adam surprised himself with this analogy. He didn't think he was able to do that. Think. That was a new one. He watched Samus shake her head, fighting inner demons only she could see. He had done what he thought was best, but it might not have been enough.

The two of them watched as she exited the ship. Rising up, like an angel of justice, she disappeared through the top of her ship, her domain. If Adam could glare, he would have done so at Sylux. He thought he knew what this bounty hunter wasdoing, but he was uncertain of himself. He needed to think about current events. Think. There it was again. Computers don't think...


	3. Federation Intervention

Kreejn sat in his chair. It was a level above the command center, in an office with a clear shield looking down into the center of business. The office was spacious, but small compared to the command center. Peering into the hustle and bustle, he saw colonels, majors, and officers rushed here and there, like little ants scurrying about working on seemingly worthless projects. That was not the case in the command center. These stupid ants were working in the most advanced center of technology the Space Pirates had: Mother Brain. She lived among them, in them, through them. She was the infrastructure that held the entire civilization together, second only to General Kreejn, for the time. He respected her, and despised her. She was needed to run the huge masses of Space Pirates, and he needed only himself to do that. He also despised Ridley. The huge, flying mass of muscle and sweat was his commanding officer, and he wanted more than that. Kraid had been a failed project, one that shamed the Space Pirates. Samus had seemingly easily overcome him, and that only added to the rage the Space Pirates felt for her. Another reason Kreejn did not like Ridley was because he was constantly bragging about how much he hated Samus. He genuinely did not know why they kept regenerating him. He was just a nuisance and an obstacle to the greater goals Kreejn had in mind for the mighty Space Pirates.

* * *

Ihkiyuk glanced up at General Kreejn's office. It loomed over the command center, a constant reminder to the personnel of the power and authority beyond their puny minds. That kept them working like mindless slaves. Not for the colony, of course not, but for their own life.

Ihkiyuk shook his head. Kreejn may hold power, but he couldn't run the Space Pirates alone. He needed an officer to do all the dirty work. That was Ihkiyuk. Ihkiyuk was the blood vessels, sending messages and handling reports. Mother Brain was the flesh, keeping muscles and organs hydrated and functioning. Kreejn was the brains, and Ridley the brawn. Together, they supported the Space Pirates. Kreejn was about to ruin all of that, taking matters into his own hands. He would be the downfall of the Pirate empire. Ihkiyuk couldn't care less. After the downfall, he would simply assume authority over the scattered, confused Space Pirates and lead. He would make a great leader. Kreejn would never become the hero he envisions himself to be.

* * *

Sylux sat on Samus's cot. She had two, and his wasn't the soft one. Rolling onto his back, he faced away from the wretched computer Samus called a companion. She would need tutoring from him, and soon. Secretly tapping commands into his arm interface, he typed a text message with coded commands to his star ship. It was to follow Samus's ship, environmental, life-support, lights and all other power supply, excluding propulsion, turned off. Untraceable, it would trail behind until needed. Rolling back, Sylux closed his eyes and tried to rest. He would need energy for later.

Adam lowered the platform into the ship, and closed the outer hatch. He watched Samus step off and walk to a panel nearby, selecting commands from the user interface. Walking back to her chair, she manually plotted an intercept course with a Federation vessel. All the while, she didn't speak to Adam, made no noise. Done plotting the course, she stood up and, after thinking about it, sat back down and dozed off. The most feared and hated Space Pirate slayer, most respected bounty hunter in her system, most useful worker employed by the Galactic Federation slept in her sleek vessel, speeding through space. Adam, her unofficial caretaker, watched silently as she slept, suit and all.

* * *

Yenk, the Federation soldier piloting the Federation craft through Federation space, felt confident that this mission would be perfect. It was simple: intercept with vessel, take cargo into custody, and fly off to promotion back at headquarters. Simple, right? Wrong. Things went wrong the second he saw the ship. It was Samus Aran herself, the huntress employed by the Federation! Suddenly, years of knowledge, rules and regulations disappeared. He didn't know what to do, should he contact her, fly by, call H.Q., fish or cut bait? He was at a loss. Thankfully, he wasn't in charge. He was just the pilot.

"Hold it, Yank. Just stop for a while," said the commanding officer in the ship, Major Tekko. He used the nickname Yenk hated, although everyone on the ship called him that.

No large screen dominated the front of this vessel; there were numerous consoles that received visual data in place of large, expensive screens. Located at one of those was Tekko, talking with Samus. After closing the link, he turned to Yenk.

"Okay, Yank. Let's go. Samus will retain custody of the prisoner until we get to headquarters. We will be her escort."

To himself, Yenk asked, _Where's the escort's escort? If this is so important, why don't we have a bigger convoy?_

His question, of course, went unanswered, and he complied with Tekko's orders. The two Federation star ships rocketed into Federation Space, with a Federation Bounty Hunter, a Federation Prisoner, and a crew of Federation Soldiers.

* * *

Samus watched space fly by through half-lidded eyes. Closing her eyes, she once again succumbed to a dreamless sleep.

Standing up, her suit glowing blue, Samus Aran stared ahead.

Opening his eyes, Sylux stared at Samus, or rather, Dark Samus. She stood facing the main screen, apparently oblivious to him. As if aware he was thinking those thoughts, she turned and walked over to him. Leaning towards him, her grinning skull shone bright in her visor, and Sylux felt a chill run down his back. He had never encountered her before, but he had gathered information about her. He knew she was to be feared.

Basking in his cowardice, Samus stood up. The blue lines that criss-crossed her suit faded to a dark marine colour, and the brightness of her skull faded. A pink flesh oozed from the back of her head to the front of her face and covered her skull. In a few seconds, Samus's face filled the visor. Her visor still remained bright blue, instead of the regular green. Still grinning, Samus leaned forwards towards Sylux. Sylux pulled back, even though a force-field separated them. Samus turned and sat back down in her chair.

* * *

Yenk piloted the Federation craft, staying slightly behind the hunter gunship. He needed to keep track of the ship beside him, and also be able to help if another ship attacked. It was relatively easy. All Yenk had to do was set a course and set a speed. No manual commands were needed; it was all automatic, and programmed into the system. He looked busy, punching in commands and fiddling with various instruments, but that was all for show. As long as he looked busy, no-one bothered him, and he was all right with that.

Suddenly, Samus pulled ahead, increasing speed. Yenk changed his propulsion to match. Slightly confused, Yenk followed Samus's craft. They were approaching Headquarters, and there was no need to go faster. Checking his radar, he saw no approaching vessels. Looking back, Samus had pulled ahead again. Increasing speed, Yenk glanced back at the radar; they were being followed.

"Ship approaching, from the rear," called the radar monitor, "Slightly below us, and charging weapons. Ship is not a Federation vessel."

Gritting his teeth, Yenk just kept picking up speed, still behind Samus. Several crew members shouted out:

"More ships are approaching. Space Pirates, from the make of them."

"Weapon systems online, ready to fire."

"Picking up speed, ships are gaining," Yenk called out.

"Change course: Split away from Samus and confront the enemy," Tekko ordered Yenk.

"Aye-aye, Tekko," Yenk shouted back, and turned the vessel as ordered.

They now faced the Space Pirates, and were ready to do battle. Samus's star ship kept going, still headed towards Headquarters. The Federation soldiers would catch up later.

"Give them a full forward blast, and hit them on the sides as we go by," Tekko sat in his chair, facing all of the activity, "We'll get behind them and target their shields."

Crew members hurried to arm the weapons and comply. The Space Pirates sped past them, not firing a single shot.

"Turn around, turn around! They're behind us, we need to protect Samus!" Tekko was excited now, bouncing on the edge of his seat. Angry that the crew didn't act fast enough, he stood up and harassed some of them for incompetence.

Yenk sat in the pilot's chair, glad that he wasn't one of the unfortunate personnel being yelled at.

* * *

Kreejn walked on a catwalk above the regeneration tanks. There was Ridley, a half-formed pterodactyl embryo in a large, clear canister below his feet. He would grow much larger, filling the tank. Fluids were occasionally dropped into the tank, usually a protein/steroid/sugar mix, but often times, a much viler fluid was deposited. That was what probably what made him so annoying, or so Kreejn liked to think.

He came to a communications booth, from which he contacted the command center.

"Ihkiyuk, how is the mission progress?" he asked.

Ihkiyuk almost wanted to shout, If you were here doing all the work, you would know! But he refrained from doing so, instead saying, "We have intercepted the convoy. Samus is putting up resistance, but reinforcements are headed towards her from Federation Headquarters. Should we pull away?"

"No, Ihkiyuk. If you could see what I can see, you would understand. But being a lowly individual, you cannot even begin to comprehend the forces at work in our empire," Kreejn replied, speaking slowly in order to further infuriate Ihkiyuk. "Besides, I have a plan."

And with that, he ended the conversation. Ihkiyuk fumed as he walked away. He wanted so badly to twist Kreejn's neck, to destroy him utterly. But that would have to wait until later.

* * *

Samus toiled at her console, sending the ship hurtling through space. Sylux, on the other hand, desperately hoped he survived this hellish trip. The ship shook as missiles and beams bombarded the fuselage.

"Federation Headquarters approaching. Federation craft ahead, charging weapons. Shields at seventy percent."

Not saying anything, Samus just kept tapping away. Adam grew concerned. She hadn't said anything throughout the entire trip. He hoped she was alright. He dared not ask her what was bothering her, for fear she would unleash suppressed emotions.

"Sixty-three percent."

Sylux gripped the edge of the bed, teeth rattling.

"Fifty-four percent."

Samus stayed at the console, entranced by the screen's glow.

"Forty-five percent. Evasive maneuvers recommended."

Ignoring Adam, Samus walked over to another wall console, keeping her balance at each shudder of the hull. Adam could not take it any more. He activated his over-ride, and applied starboard thrusters. The ship veered to the left.

Aware of the sudden change in course, and that Samus didn't have anything to do with it, Sylux realized he was cornered between an evil entity and a psychotic computer. He wished the Space Pirates would destroy them before they reached Headquarters; it would be more pleasant that way, and a heck of a lot less painful.

The ship stopped turning and set a course directly towards the space station where Federation Headquarters was located. Actually, it was a group of space stations, all orbiting a planetoid. The planetoid was the main base for Federation Headquarters, and it was heavily armed with huge amounts of fighters and ground-to-air weapons. Samus sped past the on-coming Federation back-up ships and proceeded to the nearest of the space stations.

The shaking stopped as the Space Pirates found themselves suddenly occupied with other fighter craft. Sylux breathed a sigh of relief, and relaxed on the cot. Samus never left the wall console, and kept bringing up information like the Space Pirate attack never happened.

* * *

Yenk kept the Federation ship moving as other crew members returned fire upon the enemy craft. He had been in several skirmishes, but those had been a one on one, or a two to one. This time, they were out-numbered. He tried to keep his cool, but broke out in a cold sweat as they brushed by another vessel, almost a deadly collision.

Other Federation ships were headed their way, so Yenk relaxed. There wasn't far to go to get to Headquarters.

* * *

"Call off the attack. We don't want to lose more star ships," Kreejn spoke in a microphone that broadcast the message to the entire room below him. Ihkiyuk went right to work. The whole attack was useless! Was Kreejn out of his mind? He paused to think about that. There had been no need to question the general's state of mind. It was ever so slightly obvious.

After a few minutes of establishing a link to the star ships, he gave the order to retreat. Still angry at Kreejn, Ihkiyuk stormed out of the control room. He took random halls, saluting various majors and soldiers. Finding the route he was taking familiar, he picked up his pace. Yes, this was the familiar path he had taken so many times, to the biogenetics labs. As he walked through the automatic doors, he took a deep breath. Here so many Space Pirates had altered their genome, in order to look as fearsome as they thought they were. Kreejn himself had not been able to resist the lure the labs laid out. He had injected steroids and DNA from other organisms, to inherit their traits. Each Space Pirate was different from any other, and you had an easy time distinguishing them from one another. Some didn't look too much like the insectoid species Space Pirates had originated from. Others completely changed their genome, to look and be a different species. Ihkiyuk shook his head. So many had changed that their young looked different than they used to. Soon, there would be no more original Space Pirates left. There would be different species of Space Pirates, and the colonies would separate. All because each Pirate needed to be different. Heaving a sigh, he signed himself up for a remodification. After all, what could he do about it?

* * *

Sylux prepared himself for the punishment to come inside Federation Headquarters. He had broken the stupid Federation laws so much, it wasn't worth it to try and defend himself in court. Knowing the Federation, they probably won't even have a public court. They would question him and dispose of him, just like that.

The hatch opened and the platform lowered itself to the floor of the ship. Walking over to Sylux, Samus retrieved a pair of high-level containment handcuffs from a nearby wall cabinet. Lowering the field, Samus proceeded to handcuff Sylux. He offered no resistance, knowing that this was not really Samus. Samus would be gentle compared to what Dark Samus would do to him if he didn't obey.

Sullenly obeying her silent commands, Sylux followed Samus to the lift like a beaten dog. The lift rose up, and the top of the ship swallowed them. Adam courteously dimmed the internal lights and shut down systems. He would not be needed for a while yet.

* * *

The Space Pirates had fled as reinforcements arrived. Just like them, too; fleeing from a good battle. Yenk drove the ship towards the nearest space station. He would soon be back in the barracks, with all the other soldiers. Life in space was enjoyable, if not fun. It was better than being teased and made fun of every day in the barracks. Here there were less people, and the bullies received less crowd approval for their actions. Then there were people, like Tekko, who did it anyways for fun. Yenk didn't like being made fun of; no one did. He just had to keep in mind that people are dumb, and usually don't know what they're doing. It just bugged him that people like that were usually in command.

Sliding the craft up beside the giant rotating disk, Yenk "parked" the Federation vessel onto the space station. Shutting off engines, he grabbed his supplies bag and headed towards the opening door leading into the center of Federation Headquarters.

* * *

Soldiers in Federation power suits coming back from missions, personnel making their way on errands for their superiors, and just about everyone else cleared the way for the well-known and respected bounty hunter and her prisoner. Samus had been on several space stations before, but each one was different. The room placement was the same, but there was something different about each one that made each unique. This feeling of self-importance and wonder was lost on Dark Samus. She had no need for such "feelings". The station map clear in her mind, she made her way to the prison ward. She would deposit her prisoner there. After that, she would do what she really came here for. Pushing through a crowd of new recruits getting to know the station, Dark Samus felt Samus push against the evil force that was Phazon. Quickly, she forced Samus Aran to a deep corner of her conscience, to stay.

* * *

As he was being injected with genes not his own and his muscles reinforced with steroids, Ihkiyuk realized something. Of course, it all seemed so clear now! That was why Kreejn wanted Samus so bad. It would be nice, having destroyed their worst enemy, and have her greatest strength on their side. Yes, that was why Kreejn wanted to capture Samus; it was not to use her as a pawn, it was for her Chozo blood!


	4. The Dynamic Duo

Samus walked into her quarters. It had not been touched since she had left for Tallon IV. All that seemed so long ago, even though it had only been a few months. Walking over to her bed, she sat down on the soft covers. It had been a while since she had slept in this bed, eaten meals on the table by the window looking out into space. Right now, the sun could barely be seen cresting the edge of the planet the space station was orbiting. It was beautiful, and she didn't usually have time to really appreciate the beauty when off on a mission. Lying down on the covers, she stared at the ceiling. It was a light blue, as were her walls. An overhead fluorescent light failed to add to the homely sense the room gave. Retrieving a digital pad from the night stand, Samus searched randomly through the logs it contained. Her various expansions and weapons information was stored here, and she updated it whenever she could. She then opened the category Personal Logs Entries, and typed a password to access the files. Creating a blank sheet, she titled it "Explorations of the Phazon mines." Beginning her private diary entry, she typed, _"It was a long voyage to the planet Phaaze, the home planet of Phazon…"_

* * *

Sylux, on the other hand, was not enjoying his visit to Federation Headquarters. In fact, the correct term to describe his mood was "miserable". He was currently in a holding cell, with three Federation soldiers to guard him. With no cot to sit on, he was left standing. It was a small cell, reinforced with metal alloys. Concrete was too heavy to produce in space, so the Federation was constantly developing metal substitutes. The result was a hard, durable, flexible metal that, when bent, would ooze back into place. It would hold in just about anything short of a star going super-nova. Not exactly a super-nova, Sylux was forced to remain inside the tight cell.

Footsteps clanged on the metal floor as another Federation soldier came to retrieve Sylux. The three soldiers went with them, using a soft metal rope to bind Sylux, a metal similar to the one in the holding cell. Not giving a fight, Sylux walked in the middle of the foursome, chin held high. He was not embarrassed about what he had done, rather, he was proud of it. He would do it all again in a second, if he was able to. Soldiers walking the halls stopped and stared at the group, backing away from the infamous Sylux. Some tried to clap and cheer, but it came out muffled in their suits, so they stopped. Others tagged along to see what would happen, and the crowd grew.

They soon reached a set of double doors. A security booth next to the entrance contained an un-armored guard, who let them in. The crowd stayed in the hall, peering over the threshold. They were in a well-lit room, with an operation table to one side. Monitors adorned the walls, as well as various instruments. Sylux was led to the side of the operation table. The ropes that bound his arms together behind him were unhitched and connected to hitches on the side of the table. He was laid out on the top of the table, like a frog in a middle-scholar's dissection lab. Fully aware that he might not survive this encounter with the Federation, he prepared himself for whatever might come.

* * *

Ihkiyuk was in his private quarters. Thinking about what he had found out, he realized that it wasn't such a bad idea. Using Samus's Chozo blood would give the Space Pirates amazing abilities, and with Samus out of the way, they would be nearly unstoppable. The Federation would be crushed underneath their heel, trodden on and forgotten. The Space Pirates would dominate, and a new era would begin. The Legacy of the Space Pirates. He liked that idea…

* * *

Done with her entry, Samus put the pad away. For some reason, she was exhausted. She knew that she had slept on the way here, but it seemed she had not gotten any rest at all. Lying down on the bed, she glanced at her nightstand. No picture of the forgotten past stood there, no clock with an alarm to wake her, just the digital pad. Contented with her meager possessions and no reminders of her grisly past, Samus closed her eyes and drifted off to sleep.

* * *

Taking a deep breath, the hunter lay still. His enemies prepared to take his suit, with or without his permission. He was nothing, just another dissection subject. Complete silence dominated the lab as several male humans gathered materials. Instruments in hand, the lab lights dimmed and an over-head light shone brightly on their prey. Like hawks, they descended upon Sylux, ready to tear him open.

Suddenly, terrified shouts came from beyond the double doors. Several gunshots went off in the hall, and soon all became silent once again. The surgeons stopped, and put down their tools. One reached for a cabinet on a nearby wall, but froze as an alarm went off. Loudspeakers shrieked, and various lights flickered. A blast door lowered over the double doors, effectively sealing the room and its contents. The dimmed lights turned back on, illuminating the startled doctors.

Shots began to sound outside in the hall. They stopped, to be replaced with the sound of crunching metal. The blast door began to disintegrate, smoking parts falling to the floor. The frozen surgeon suddenly leaped into action. Grabbing at the cabinet door, he whipped it open and seized one of the energy assault rifles hanging on a rack inside. Turning around, weapon charged, he lowered the gun and…exploded. A missile hit him smack in the face, sending bits of doctor all around the room. Blood gushed from the headless body as it fell to the floor. The other surgeons just stood next to the table, dumbfounded. A blue figure walked towards them, arm cannon at her side. Hand outstretched, she touched one of the humans. The doctor leaned over Sylux, dead. One of the two left in the room alive made a break for it. Running past Samus, he was almost to the door when Samus took aim and fired. The result was not pretty. The remaining doctor had grabbed a weapon from the storage cabinet and taken aim at Samus. Two shots sounded out, three, four, and the shining blue figure turned towards him. Walking over casually like mosquitoes were trying to ram her, she grabbed the human by the neck. The expert surgeon, well known and looked up to by peers, fell dead to the floor like a pile of rags. Facing Sylux, Samus bent down and touched the metal bonds that held him in place. They shriveled up and melted from her touch, releasing Sylux. Sliding off the table, he dropped to the floor. Grabbing the fallen rifle, he followed Samus out of the lab room. Sirens blaring and lights blazing, the two bounty hunters ran from their enemy, the Galactic Federation.

* * *

Spire traveled in his heated ship, searching. Searching for something, anything, pertaining to his race's whereabouts. He had traveled to the Alimbic system in high hopes of obtaining the Ultimate Power that lurked there, but he had failed. He had failed his race, his species. It was not his fault, he knew that, but he felt responsible somehow, for not being there, not being present when they disappeared. He had been lucky to find his ship still intact. It remained operational, but barely. Most of the systems were malfunctioning from some sort of radiation he could not identify. His computer log entries stayed intact, however. They were small files, and had not been destroyed with most of the ship's memory. He had written many entries since that memorable day. He wrote in hopes that, if he failed to find his species, someone would find his ship and pick up his search where he left off. He wrote very detailed entries, many details unnecessary, but he wrote them anyway. He had stopped by any inhabited planet he could find, trying to find information. He felt himself drawn back towards the Alimbic system. He felt that there was something there, something he had overlooked when he had fled weeks ago. Nearing the Alimbic cluster, he scanned for any ships nearby. None, but the radar was malfunctioning. No ships appeared on the screen, but no planets either. He left the panel to return to his quarters, leaving the computer with a constant radar search. He would come back later, after he had something to eat. The last survivor of a civilization had to eat something, you know.

* * *

The two bounty hunters sped away from the doomed space station. Sylux shook his head. The last minutes seemed a blur to him, but he could remember the basic sequence of events. After he had been rescued, he ran back to Samus's ship. Priming the ship, he waited for Samus to get back. In the mean time, he fending off soldiers trying to get to the ship to stop them. All in a day's work. Samus had come back soon, and had taken command of the space faring vessel. Blasting away from the Federation station, Sylux looked back. She had messed with the orbit trajectory of the colonized station, and it now spun out of control. Several large vessels attached themselves to the huge mass of metal, to try to stabilize it. It was working, both to save the station, and to provide a distraction as the duo escaped.

* * *

Turning in her chair, Samus looked at Sylux. She leaned back, arms on her chest. She was still in her suit, and still had the blue tint in her visor. That slightly concerned Sylux. Sighing, she said, "You know who I am. I know who you are. Why are you following Samus Aran?"

Sylux was startled to hear her speak in third person. _She_ was Samus Aran, but, then again, not really…

"Why should I tell you? I have no reason to trust you," Sylux regretted saying this the second the words came out of his mouth. He should trust her, especially after that strange display of power in the lab, and, after all, she had rescued him.

Samus laughed. The sound sent shivers down Sylux's body.

"Now you're resentful I saved you? Pity, I was hoping I could pry some information out of you before I killed you, but, seeing as I have no choice now…" as she said this, she reached for him.

"Stop!" Sylux shouted. The hand froze. "I, uh, well, was employed by the Space Pirates to kill you. I was supposed to bring your dead body back to them. That never really happened, so, I guess we're together in this."

Samus withdrew her hand. "If you think we're together, think again. _You_ shall serve _me_. I will keep you until I see fit to dispose of you. Samus, on the other hand, wishes to kill you right now. I am being generous, and you should accept those terms before I reconsider."

Sylux only nodded. More rebellion would end his life.

"Shake on it?" she inquired, stretching her hand out again. Sylux backed away, shaking his head. Samus threw back her head and laughed. The sound moved Sylux to nausea.

* * *

Spire was feasting on compacted vitamin mix, which he personally called "sludge." Next to it was a tube of paste, full of proteins and nutrients his species depended on. He thought it was disgusting. It was much better made fresh, and not mixed together. And before the expiration date. That would help a lot. He was thinking about homemade meals when an alarm went off. Rushing back to the cockpit, he glanced at the radar. No planets had appeared, but a lone ship had. Sitting in the middle of the two planets and space stations, he checked visual. It was fuzzy, but he could make out Federation markings on the hull. He did not know much about the Federation, but he did know that they ruled a large portion of their known space. That included his home world. That they owned his planet without his permission infuriated him. He would engage in combat with this vessel, no matter how badly it damaged him.

The vessel had obviously spotted him, for it was coming straight at him. They were trying to establish contact, but Spire's damaged systems prevented him from receiving any transmissions they sent. He charged weapons, ready to fight.

The Federation craft, sensing an oncoming attack, charged their weapons as well, but not fast enough. Spire zipped in close, hitting them with a full spread of missiles and beams. Some weapons were not operational; he would have to fight without them. The damaged Federation ship was a scout ship, meant for a quick skirmish, then to get out of the fight. It had low shields, so it took heavy damage. Crippled, it turned and shot rear beams towards Spire. Spire's ship took the full brunt of the attack. Several shield generators, due to radiation degradation, failed, and Spire was defenseless. He too turned and fled. Seeing he was fleeing, the Federation ship followed close behind, to see what Spire would do. Knowing he had a promise to find his people to fulfill, Spire did not respond to the last shots. He headed towards the last coordinates of Oubliette, where he had failed to obtain the Ultimate Power. A new reading flashed on the radar. It was a massive rip, tendrils of energy flowing from the center. Sylux checked visual readings. Nothing of the sort appeared. Thinking that the radar was malfunctioning again, Spire kept going. The Federation ship, for reasons of its own, fired one solitary missile, possible a warning shot, at Spire. He prepared himself for death, but it never came. Instead, the missile imploded behind the ship. There was silence as both ships continued, though no thrusters were applied. Spire's ship stopped, then was gently pulled backwards. His thrusters were going haywire; they weren't responding. The ship gradually sped up, until it hit something. Not the Federation ship; it had turned tail and fled. He applied thrusters; no response. Whatever Spire was being sucked into, he knew it wasn't good.

* * *

"Federation ship Hetle Falcon 2927 contacting Federation vessel 2482, do you copy?"

"This is Util Kikl, 2482, what do you want, Falcon?"

"We have entered the Alimbic System. We engaged in combat, and…"

"Details for the report, Falcon. What do you want?"

"The enemy ship disappeared, Kikl. It just disappeared."

"Radar?"

"None. No radioactive activity, nothing to mess with the sensors. Visual was lost, as well."

"Well then Falcon, contact Federation Headquarters. Let them know what happened. We'll be over in a few minutes."

"Roger that, Kikl. Position is static, we'll let you know if anything happens."

* * *

Samus rushed through various waves of unsuspecting vessels. The commotion with the space station was enough for them to escape unseen. Their signature was lost with all the others as ships fled or zipped closer for the action. Weaving in and out of trade ships and small voyage craft, Samus set a random course in order to further confuse Federation security ships. She sat at the interface for a while even after they had cleared the worst of the mass of ships. Sylux explored the interior of Samus's ship. It was sparsely decorated, with lights lining the domed ceiling edge. Two bunks lay on opposite sides of the ship; there was no other room other than the main one. Other than the cabinets and the door that lay in the direct back of the craft, there were no hatches. A fold-out table was near each cot, within easy reach of the bed. Sylux opened the door in the back. Quickly shutting it, he sat down. He wished he had not looked. Space toilets were so much more different than normal ones. He would rather wait until they landed somewhere.

Turning in her chair, Samus stood up and walked towards Sylux.

"We are now undetectable; I've removed all the tracking signatures, and currently this vessel is no longer Federation. It will be seen as a custom leisure ship. The Federation will have a hard time finding us. I have tapped into the communications network: we can hear all transmissions from Federation craft."

"Interesting," Sylux responded only half listening. Still examining the ship, he wandered from one panel to another. Tapping one with a peculiar nozzle port, he stood there for several minutes searching random information.

Shaking her head, Samus returned to her chair. Leaning back, she realized she hadn't switched out of her suit. Glancing at Sylux, she figured he wouldn't mind. After all, species don't usually have romantic relationships with other species. They just didn't work out.

* * *

Spire woke up floating inside his ship. Woozy for a few seconds, he quickly recovered. Realizing he was floating, and not standing, proved difficult for him to grasp. He had not been weightless in space before. He had been trained, but not for this sort of thing. Figuring that the magnetic applicators in the ships flooring had gone offline, he stayed floating inside his ship. Reaching for a wall, his finger brushed the solid surface and sent him slowly rotating towards the other side. This was going to take a while. _BEEP_ An alarm went off at his console. Unable to see the screen, Spire called out in a deep voice, "Computer, audio."

Responding, the computer replied in an automated voice, "Sh-fft-p appro-zt-ing, unkno-on or-zzt-in. Rec-zzt-ende-fft-ction?"

Barely able to understand the fuzzy recording, Spire called out again, "How long have we been at our present coordinates?"

"Drifft-ng for zzt-arly trree oors. Prrei-zznt loc-fft-ion uuown. Lle-fft kn-zzt cooorororor--"

The computer froze up and shut down. Lights shut off and returned in a low red color. He was running on emergency power now. The main screen flickered and showed a fuzzy image of a strange vessel approaching. Then it, too, shut off. Bathed in red light, Spire floated in unknown space. He thought about his family, wondering if he would ever see them again, enjoy a home-cooked meal with them. He might never do that, but he could at least try to make it possible. The ship shook as the alien craft attached itself to Spire's. They were here, whoever 'they' were.


	5. Escape

So sorry about the lateness of this chapter… I have had a lot to do lately, and pleasing my large fan crowd isn't, unfortunately, top of my priorities list. Feel free to send in a review; they are always accepted. (Unless, of course, it is very sarcastic and/or offensive to me, the writer)

* * *

"RED ALERT! RED ALERT! THIS IS NOT A DRILL! REPEAT, RED ALERT! ALL HANDS ON DECK! ALL HANDS ON DECK!"

The loudspeaker blared as armoured Federation soldiers hurried to their stations. Yenk was not one of the soldiers in armour, instead dressed in his gray Galactic jumpsuit, complete with a large logo on his breast pocket. He ran down circular corridors, running upwards and forwards. The shape of the large, disk-shaped space stations were made to mimic gravity by spinning like a top. This made life easier for crew missing home, but looked old next to today's top of the line gravity-simulating decks.

Yenk stopped at a large pair of double doors. A red bulb above him pulsed bright red, bathing Federation crew in a blood-red light. A keypad sat on the wall next to the doors. Yenk reached for it, and typed a specific password, used only in emergency situations. Other codes did not work during emergencies; a special code had to be used. The keypad gave a _busy _signal, and then presented Yenk with _INCORRECT CODE_. Yenk frowned and tried again. By this time, others in his team had surrounded him, including Captain Tekko.

"Step aside, Yank. Let me try," Tekko then walked up to the keypad as Yenk stepped away. Tekko punched in a different password, but he, too, was rejected.

"Something isn't right here," Tekko said.

Yenk rolled his eyes. Of course something wasn't right! He turned to the other crew members. One of them had a hand blaster, not nearly enough to knock the door down.

"_EVACUATE IMMEDIATELY! REPEAT, EVACUATE IMMEDIATELY!"_

Yenk swallowed. This wasn't good. He turned and ran in the direction of the hangars. The crew, seeing Yenk run, turned to do so as well. Tekko, realizing he had lost control of the situation, joined them at the back of the group. They ran alone down the slanted hall; everyone else had run past them. Fortunately, they were on a hangar level. They reached the hangar doors. Someone had punched a sizable hole in the middle of the double doors. One by one, they climbed through. As they emerged, they realized that they really were the last. One ship remained. A ramp leading up into the belly of the large Federation craft provided an entrance. Single file, they jogged into the ship. Someone closed the ramp, and Yenk revved the engines. The large bay door was wide open, revealing a black infinity. The ship slowly rose above the floor, pushed up by large, flaming thrusters It then turned and glided out of the abandoned hangar, gradually speeding into the endless void.

* * *

"What are we going to do about Samus?"

"I don't know, Admiral. She disobeyed orders…"

"More than once…"

"…and she is very unstable."

"Very."

"She just endangered millions…"

"Billions…"

"…of humans, destroying networks and threatening our alliance…"

"a very helpful alliance."

"Yes…very helpful, Admiral."

"Well, I suppose she has outlived her potential."

"Very much so."

"So, we shall have to kill her."

"She ran off…"

"…making it easier for her to disappear…"

"Into the statistics of spatial accidents that occur each month…"

"Yes, that would work, Admiral."

"Thank you, Admiral."

"I shall get right to work on preparing a team to track her…"

"She is very resourceful…"

"…she will try to hide…"

"…but she will fail."

"Yes, fail. We will find her."

"And when we do…"

"…she must be punished."

* * *

Kreejn did not know what to make of it. There was Ihkiyuk, with bulkier arms than usual, ordering personnel around in the command center. He strutted around like he owned the place. Kreejn smiled. He would have to teach Ihkiyuk a lesson. Suddenly, a soldier walked up to Kreejn and handed him a note.

"What's this?" Kreejn demanded.

Saying nothing, the soldier walked away, and was lost in the crowd of other soldiers. The soldier had looked very plain for a Space Pirate. The usual shoulder spikes and spiny armour were common around Pirates these days. But he had worn a blue uniform. Bright blue, like… no, what was he thinking? That would be impossible. Samus had been spotted in Federation space, nowhere near their area. And yet, the possibility lingered. Shaking his head, he looked at the paper. Why hadn't they called him on the intercom system? The folded paper was tainted yellow with age. Unfolding the crisp parchment, General Kreejn stared in bafflement at the words. It was a clip from an Earth newspaper. He could tell because it was in English, the most common Human language. There was a picture in the middle of the main article; it depicted several Federation troopers battling Space Pirates. Many Space Pirates were on the ground begging for mercy, or dead. Another picture showed a Human, smiling at the camera. The caption assigned to the picture was:

_Federation Troopers combat the deadly Space Pirates on Tallon IV. Soldier Entern, pictured left, survived that bloody day in history. We will remember this day with reverence, the day the infamous Space Pirates were defeated, with the help of t--_

The caption cut off; age had claimed the rest of the article. Kreejn looked at the Human. Entern was a handsome Human, by Human standards. To Kreejn, he was ugly, despicable; just another Human. Folding the paper back up, he realized something. Tallon IV? Space Pirates defeated? That was not possible. Re-opening the paper, Kreejn stared at the text. He was fluent in English, and he could read some, but not write. There, to his amazement, were the words he thought he had imagined. The article was old, but the date had been left out. Kreejn realized something else. Earth didn't use paper for newspaper anymore; it was all electronic now. This was _very_ old, older than any Space Pirate alive. Of course, that didn't say much. With the war with the Federation, soldiers didn't grow old. They just died in battle. But even so, Kreejn would have to date the material. Carbon dating was irregular and spontaneous, a lesson the Space Pirates learned from Human error. He would take this back to the labs to test for himself. He wouldn't show it to anyone, especially Ihkiyuk. No-one was to be trusted.

* * *

Samus sat in her chair, apparently asleep. Sylux remained on his cot, where he had kept his distance for the last ten minutes. Samus jerked in her sleep, and sat up. Looking at Sylux, she said, "You're wondering how I killed the Federation soldiers."

Sylux did not move at this accusation. He simply sat there, staring at the wall.

"Samus has absorbed many a creature: the Metroid, the X, Chozo blood, and, of course, Phazon. I can use their unique abilities, unlike what Samus could do. She could control little of their full potential. I have used the X's ability to morph into other creatures to my advantage. That is how I appear human. With the Metroid, I can drain organisms of their life force."

Sylux continued to stare at the blank wall, but fear coursed through his body. If she were that powerful, they could take on the entire Federation with her alone! But, if that were possible, then why hadn't they done that already? He turned to her.

"Why didn't you wipe out the Federation right then and there? You had the chance. Maybe you have a soft side, after all…" Sylux said this slowly and clearly.

Fast as lightning, Samus jumped over to Sylux, her figure a blur in the single bound. Gripping his neck in her left hand, she growled, "What's stopping me from destroying you right now?"

Dangling from Samus's tight grip, Sylux struggled to free himself. Sucking in breath, he managed to squeeze out, "Ph-phazon…"

Dropping him like a doll, Samus glared at Sylux behind her blue visor, "Correct."

Walking back to her chair, she motioned for Sylux to sit down in the other command chair. Cautiously moving towards the chair, Sylux watched Samus carefully. Sitting down, Samus said, "Yes, I need Phazon in order to utterly destroy the Federation. Unfortunately, Samus destroyed the planet Phaaze, the main source of my power. I have felt another energy source not unlike phazon, far away in a sector known as the Alimbic system. It won't be in our dimension very long; it is highly unstable. We must move quickly in order to insure our claim."

Turning to her console, Samus went to work on typing out precise coordinates on the main screen. Staring at her, Sylux leaned back in his seat. Things were just getting weirder and weirder around here.

* * *

"You want me to do _what?_"

"I want you to date this material. Now. It is a matter of urgency," Kreejn was getting impatient. This was taking too long. He had other things to do besides stand here all day, talking to an incompetent lab rat.

The Space Pirate soldier, dressed not in armor, but in a heavy black and red coat, took the tiny, ripped material from Kreejn. He withdrew a peculiar-looking instrument from a large pocket that dominated the front of his unusual uniform. Holding the tool up to his right eye, he distanced the yellow paper a few inches from the other end of the tool.

Muttering under his breath for a minute, he finally glanced up at Kreejn, who was obviously expecting something.

"Can I help you?"

His temper spent, Kreejn yelled, "HOW LONG ARE YOU GOING TO TAKE!?"

Offended, the scientist quietly put away his instrument.

"I will need a while to study this particular item. It seems to be very old, maybe part of some ancient parchment. It needs to be tested. Come back in a week, maybe two."

"I DON'T HAVE A WEEK!! I NEED IT NOW!"

Stretching out his hand to Kreejn, the Pirate presented the paper, "Maybe you'd like to date it, then."

During the whole commotion, several scientists had turned towards the two. Others had looked around from behind workstations, concerned about the argument. Kreejn snorted at hand, and turned to leave. Walking to the door, he pushed down a young Space Pirate carrying a tray of bottles, each holding a strange liquid. The Pirate went down, and the bottles went flying. Each scientist flinched at the sound of the breaking vials, and several stood up, ready to help clean up. Kreejn opened the door and stormed out. The scientist with the paper stood where he was. Shaking his head, he turned to a nearby workstation.

* * *

Adam studied the new Samus. He had sensed something was different about her when she had boarded the ship, but he didn't know what. Now, though, he knew. He knew that this was Samus, and yet, not. The Samus he knew was gone, to be replaced by her evil twin. He would serve Samus, but not this _thing_. Adam would wait until Samus found a way to contact him. For now, he had no plan of action. He would just act as stubborn as possible.

The lights dimmed inside the ship. The familiar hum of the engine clicked off as systems powered down. Samus glanced up. Looking around, her gaze fixated on Sylux. He shrugged.

"Wasn't me."

Glaring at him, Samus turned to her blank console. The computer was being very, very annoying. How could Samus live with such a thing? Pounding the keypad, she stood up and began pacing around the ship. Sylux watched in half-amusement.

"At the rate we're drifting, we should be able to make it there in time, but if we encounter anyone, or anything, we're dead."

Sylux just nodded as Samus walked around.

"Our momentum will carry us, but we'll be bypassing a planet on the way. Its gravity might pull us in, but it might not."

Her pacing grew faster, and her suit clacked against the floor. Sylux opened his mouth, "But if we encounter someone…"

She stopped and looked at Sylux. He cleared his throat, and began speaking again.

"…then we might take their ship, and, problem solved."

Sylux looked up at the towering Samus as she digested this new thought.

"I might keep you around awhile yet, Sylux."

With that, she went back over to her console. With the ship so dark, it was hard to see what she was doing, but bright sparks appeared across her suit, hissing and crackling. The blue electricity traveled down her arm, and connected with the console screen with an explosion of sparks. Almost immediately, the console glowed a dark blue. The glow illuminated the ship a little. Samus sat down and typed commands. Soon, she was done. She stood up and the screen went black.

"There. A vessel is on its way, to rescue two stranded space-traveling merchants with a valuable cargo. They will be here soon."

Sylux stood up and said, "Then we should prepare. May I have my weapons back?"

Samus stared at Sylux for a while, and, without breaking her gaze, replied, "I suppose."

Sylux walked over to a cabinet on the far wall. There was a keypad, but, with most systems shut down, was useless. Not caring anyways, he simply tried to pry open the air-tight cabinet. Seeing Sylux struggle hopelessly with the wall, Samus walked over and brutally pushed him aside. Raising her arm cannon, she smashed a gaping hole into one side of the cabinet door. Broken wires popped out, sparking at the ends. Reaching inside, she grabbed the dual arm cannons and tossed them one by one to Sylux. Catching them, he immediately ran a visual damage check on both weapons. Not a scratch.

* * *

Flippant young scientists. Always thinking they were better than everyone else, always talking smart. Kreejn had just about had enough of all of this. He was on the verge of going insane in this small station with too many people. Kreejn reached his quarters and opened the door. Looking into the small room, he realized just how cramped it was. Three other captains' bunks were squished to one side, and a table on the other. It didn't even have a toilet, much less a place to bathe. Those were all public facilities now, and were always crowded and smelly. Letting the door close, he stomped down the hallway. He needed someplace to vent his anger. Stopping short, he saw Ihkiyuk talking with another officer. Or some_one…_

* * *

The man sighed as he drew close to the drifting ship. This cruise was for luxury only; it was his well-earned self-given weekend to himself. He didn't need something to cause him grief on his vacation. Peering at the small ship on his monitor, the plump man wondered how it could contain such a priceless cargo. But, if he saved it and the important people on board, he would be seen as a hero. Smiling smugly to himself, he delicately pulled his ship up next to the other. Positioning his ship on top of the other, he let down a thick tube that attached itself to the roof of Samus's starship. They were connected. He then opened his floor hatch and waited. He didn't have long to wait.

* * *

Sylux watched space go by through yellow plastic. He wasn't in the best mood. Carrying equipment was _not_ his version of fun. This was his fourth trip to the traveler's ship, and still Samus hadn't moved from the man's console. As he arrived, he flinched when he saw the bloody carcass of the wealthy man in the lounge. Why did Samus have to be so brutal? Walking out of the room, he proceeded to the cargo hold. Here, Samus's suits lay on the floor. Several large Federation containers were scattered about, and Sylux put down the one he was carrying by the door. Closing the door behind him, he collapsed onto a nearby sofa. Inspecting the furnishings, he guessed this human was straight from Federation space. Upon looking at the bottom of a well-stained mug, he found he was correct: printed in large letters, it said MADE IN CHINA.

Sylux heard footsteps approaching. Putting down the mug, he glanced up. There was Samus, in her blue jumpsuit, exiting the small cockpit. Not even bothering to look at Sylux, she made her way to the opposite side from him and walked out of sight into a private bedroom. The door slid shut behind her. Heaving a sigh, Sylux pried himself out of the comfortable sofa and went to his designated room. They were moving fast, fast towards an unknown adventure, to go where no man has ever gone bef—_BEEP BEEP BEEP._ Sylux frowned and looked at his wrist. A little blinking light told him that he had a message. Selecting it, he saw the following message from his gunship:

_Proximity aler. Federation ships closing in. Evasive maneuvers initiated._

Muttering a few curse-words under his breath, Sylux shut down his suit for the night. He would work out the situation in the morning.

* * *

Spire woke up dizzy. He couldn't feel the rest of his body. He tried to lift his arm. No success. Right now, he wasn't sure he had an arm to move. He then concentrated on moving his head. Again, he failed. Frustrated, he stared straight ahead. There wasn't much to see. A bright light shone directly into his eyes. Spire squinted against the glare. He could make out faint shapes…

Suddenly, the light blinked off. Startled at this change, Spire closed his eyes to the dark. Opening them again, he saw that dim lights had turned on. There was movement to his right. Looking that way, there was nothing. To his left… Spire looked to his left. Again, nothing. Maybe his eyes were playing tricks on him…

He felt the floor move beneath him. Some feeling returned to his neck, and he strained to look down. He was strapped to a table by thick straps. The table was slowly inclining upwards, and stopped when it had reached a vertical position. Letting his head rest, he again saw shapes moving in the dim light. Shaking his head, he looked again, and his breath caught in his throat. There, a bulky figure stood in front of him. As his vision cleared, Spire saw that he was behind a clear wall. The dark figure behind the wall lifted a device to his head, and a deep voice sounded above Spire.

"Are you all right?"

Blinking, Spire managed to nod a yes. The voice was very loud, and it hurt his sensitive ears. Moving his mouth, he tried to speak.

"hooore eere yoo…?"

Seeming to understand, the figure spoke again.

"We are who you are."

Confused by this answer, he thought for a minute. Then, it came to him. As recognition lit up Spire's face, the figure spoke, "Welcome home, Lost One."


	6. Another Frontier

Author's Note: Uhmm…yeah. Really sorry about this chapter. I was supposed to really work on CIC during the summer, bu-ut…never really got around to it. Again, I apologize for this inconvenience. As promised, I have released the final chapter for the 1,000th visit to my story.

* * *

General Kreejn sat in his office that overlooked the command center. Tonight, the room was nearly empty. Most personnel had gone back to their quarters to get some of the measly six hours of sleep they got each 36 hour day. Kreejn was restless. Waiting for the test results was taking longer than he had expected. He sat back in his chair, then sat up again. He fiddled with his computer. Then, a beep from the door. Anxious, Kreejn quickly stood up.

"Come in."

Calming himself, Kreejn smoothed down his black and red uniform. The door slid open. Ihkiyuk stood in the doorway, looking slightly shameful.

"What do you want, Ihkiyuk? It's late. Even I need sleep."

"I came to give you my thanks, for being a strong general when there was little hope left for us…"

Kreejn was surprised. This was a change in Ihkiyuk he could appreciate. He walked over to the officer in the door.

"Well, we all know I can't do much without a commanding officer to look after my men. You have done a wonderful job, Ihkiyuk. You will retire a happy man."

Ihkiyuk squinted his black, beady eyes, "Not happy enough."

With that, Ihkiyuk whipped out his sidearm. But before he had a chance to fire, Kreejn stepped forward and knocked the gun out of his hand. Kreejn then grabbed Ihkiyuk and wrapped his arms around him. Ihkiyuk struggled, then stopped.

"I meant what I said. If you hadn't gotten cocky, things might have been different, Ihkiyuk. But now, you'll have to go."

Kreejn twisted Ihkiyuk's arm until he heard the satisfactory snap. Ihkiyuk cried out in pain. Dropping him, Kreejn calmly bent down and retrieved the small energy pistol. Still crouching, he put the weapon to Ihkiyuk's head and pulled the trigger. The Space Pirate fell to the ground, dead. The scent of burning flesh would linger in the room for weeks. He would have to get a clean-up crew in here the next morning.

* * *

Sylux opened his eyes, drew in a large breath and sat up. He was sitting on a large, plush bed with elaborate designs on the covers. Fanciful wall decorations covered the wall opposite the large, circular window looking out into space. Swinging his legs over the edge of the couch, he reached over to the night stand and retrieved his other sidearm. He had kept one at his side, primed and ready for action, should a problem arise.

A small notice flashed in the corner of his head's up display. It was the message from his gunship that he received before he had slept. He opened it.

_Federation ships avoided successfully. The ships destroyed Samus Aran's gunship after detecting no life-signs aboard. Federations ships are currently in orbit around the planet Ureis, in the Quadrant H-34-16._

Sylux shrugged off the news and deleted the message. Walking to the door, he stood in front of the sleek, silver door. Reaching for the keypad, he typed the code he had typed last night to lock the door from the inside. Nothing. He glanced up at the motion sensor above the door, frowned, and typed the code again, letter for letter. Still nothing. Grunting, he backed up several paces, switched to his missile launcher and pointed his arm at the door.

* * *

Samus sat in the cockpit, flipping through the ship's logs, deleting them as she went. A muted explosion came from the main lobby behind her, and a few moments later, Sylux walked in.

"I don't appreciate being locked in my own quarters," Sylux said as he took a seat behind her.

"It was for your own safety, Sylux," Samus quietly replied. She continued to look through the logs, and, finding nothing interesting enough to keep her occupied, turned her chair around to face him.

"We have approached the Alimbic system. Your assistance is no longer required," she said as she reached an arm out to him. Jumping out of his seat, Sylux avoided Samus's long reach and exiting in to the lobby.

"Don't play games with me, Sylux. You know it's all useless. In the end, you can't hide from me."

Ignoring her, he charged his missile launcher and waited for the cockpit door to open. Instead, the door started glowing a bright blue, and tendrils of blue plasma shot out of the door towards Sylux. Diving to the side, he shot at the door. The explosion disintegrated the door and revealed the bright blue outline of Samus, standing in the smoke and dust. The tendrils shot for Sylux again, and caught him in their grasp. Puslses of energy started flowing out of Sylux and into the tendrils. Samus laughed as she absorbed the pulses. Sylux had difficulty breathing, and soon, couldn't move at all. The room swam in front of his eyes, and all became black. Suddenly, the speaker system started blaring:

_Warning! High levels of radioactivity surround the ship. You are advised to initiate an evacuation. Warning! High levels of radioactivity ..._

The ship gave a jolt, and the lights inside the ship winked off. All that remained was the image of a bright blue skull smiling the grin of death in the darkness.

* * *

Spire lay on the metallic bed, still bound by straps. His only visitor had left a long time ago, promising to return soon. He tried to collect his thoughts, trying to piece together what little information he had. After a while, he tired of this and closed his eyes to rest.

"Spire? Can you hear me?"

Spire's eyes jerked open. He strained to sit up and tried to get a better look at the figure behind the transparent wall, but soon gave up. He was so tired…

"Spire, I'm sorry to have kept you so long, but I have been kept busy. I am reluctant to tell you this, but the radiation that damaged your ship can also be harmful to us. We have to keep you inside this room until we can find a way to help you. Do you understand?"

Spire gave a slow nod.

"Good. We are going to run some tests right now, so please stay still for a while."

Spire could feel sleep wash over him. His last thought was about home, and how long it had been since he had seen his own people.

* * *

Samus was awake, but kept her eyes closed. She was now back in control of her own body, and she could no longer feel Dark Samus' presence. Letting her eyes open just a little bit, she could see she was floating horizontally inside a large tube, with liquid all around. A breathing apparatus had been wrapped around her mouth and nose, and several tubes had been inserted inside various parts of her body. Samus checked and realized she was still inside her zero-suit. She then closed her eyes, in part because the liquid stung her eyes, and because she was so tired…

Quickly, her eyes snapped open again. She mustn't let herself become vulnerable. Reaching out a hand, she touched the surface of the tube. It was warmer than the liquid around her, and though she couldn't explain it, it almost felt _alive_. Hearing a door nearby _whoosh_ open, Samus let her body go limp and her hand drift away from the tube wall. Closing her eyes, she could hear muted steps of someone approaching the tube. Silence. Samus cracked open one eye and turned it to a side. There was a dark figure there, turned away from her. The liquid shook, and a sucking noise commenced. Samus felt herself sink inside the tube as liquid drained out of it. The tube completely drained, Samus lay on the bottom of the warm cylinder. She panicked as suddenly, the surface beneath her gave way. She slid out of the tube and onto a metallic surface. She could now hear clearly numerous shuffles and grunts as the surface she was lying on moved. Tensing her muscles, Samus prepared to attack.

* * *

Dark Samus opened her eyes, but could not see. She tried to move, but found she could not. Confused and angry, she used what little power she had left to lash out. Nothing. The only thing she could do now was to wait. Wait for an opportunity to arise. For now, she rested.

* * *

Opening her eyes, Samus looked down near her feet. A man was pushing the cart she was on. Kicking out, she struck him in the face. A grunt, then a thud as he hit the floor. Samus sat up. The tubes were still in her body, and they hurt. They were connected to the table itself. Puzzled, Samus quickly tore one out of her. It hurt, but the tube didn't penetrate far. She took the rest out and removed the breathing apparatus. She climbed off the cart.

The man that was pushing the cart wasn't a man at all, but an alien. It looked slightly human, with two arms and legs, but the arms were notably longer and thinner. The face had two large eyes, closed presently, and large slits covered the rest of the face. Every so often, the slits would move, indicating the subject was breathing, and was still alive. Looking around the rest of the room, Samus could see she was in a holding cell. Against one wall, the tube that had contained her minutes before. On the ends of the tube, there was not machinery, but organic masses. Samus shuddered. The rest of the walls were a plain dark grey. The only other object was the door. Bending down to the alien, Samus searched for a firearm. Finding none, she checked for a cardkey, or something. Still finding nothing, she stood up and walked to the door.

The door slid open with a quiet _hiss_ and Samus proceeded cautiously.

* * *

The figure behind the transparent wall watched Spire as he slept. _Pitiful life form_, it thought, _it has such little intelligence. Easily confused by a few hormones and disillusions. All shall be revealed soon, my pet. Revealed, indeed._

* * *

Samus crept down the well-lit hallway. So far, there was no sign of life, no noise at all. The alien could have been alone here, wherever here was. Unlikely, but definitely possible. There were no signs of damage to the hallway, but also no other doors. Samus grew continuously more paranoid at the silence, her footsteps seemingly echoing through the halls.

Suddenly, she found herself in front of a door at a dead-end. Again, there was no security devices attached anywhere. Strange. The door slid open when she approached it, revealing a dark room. She walked into the room in a slight crouch, ready for action. Her acute eyes adjusted quickly to darkness. She was in some sort of control room, with several glowing monitors on workstations. There were stations for numerous beings, but none were present in the room. Walking towards what seemed like a main console, Samus inspected the controls. Definitely not what she was used to, but usable. Sitting down in the too-small chair, she began exploring the computer.

After quite a while, maybe an hour or two, Samus found something interesting: Spire. The screen Samus was looking at showed Spire on a table, strapped tightly against it. A dark figure standing behind the far wall was apparently watching him, not moving for a few minutes. Then the figure reached out and typed out a command on a console that was out of sight. Suddenly, Spire jerked and fell limp. A green icon on the screen suddenly winked out. Samus stared at the screen. She could only surmise that Spire was dead, and that the alien had killed him. Slowly navigating back through the network, Samus thought more and more of Spire. For what reason did Spire die? Had he been in pain? All sorts of emotions flooded back to her, emotions she had suppressed ages ago. The pain and remembrance…no. She could not afford to lose concentration now. Quickly, she buried the emotions deep in her consciousness and continued to try and find something of value in the endless garble that was on the screen.

* * *

A _whush_ of air followed Samus as the door closed behind her. She ran up to one of many small fighter ships in the hangar, looking warily over her shoulder. Climbing into the open cockpit, Samus looked at the strange controls. Guessing at buttons, she managed to start the engines. Certain some form of security would catch her, she fumbled with the controls. Sending commands to the main computer system, the hangar doors, which spanned an entire side of the hangar, started to open. The vacuum of space sucked out debris in the hangar and Samus's hair blew in her face. Closing the hatch, she released the spaceship from its docking clamps, sending it and herself careening out into space.

Later, still struggling with the foreign controls, Samus thought back to the computer. How she had finally found the station's map was beyond her. Glad to be away from it, Samus glanced behind her back at the station. There it was, a dark blot against the black of space. Seemingly formless, it carried a shroud of mystery around it. Samus knew she might never know what really happened there, or why Spire died, but she did know that she would find out to the best of her abilities. Maybe it was a secret Federation project, or maybe even the Space Pirates were behind it. Maybe it was something else entirely.

_To be continued…in another story._


End file.
